Contacts of the strand formed by residues 258 - 265 (chain A) in PDB entry 1W21
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A TRP* 3.1 35.1 + - + +
226A ALA* 4.3 6.5 - - + -
249A THR* 3.7 1.3 - - - -
250A ASP 3.0 32.1 + - - +
251A GLY* 4.6 0.2 - - - -
256A ARG* 4.7 4.7 - - - +
257A ALA* 1.3 71.3 - - - +
259A THR* 1.3 63.0 + - - +
260A LYS* 5.0 4.9 - - - +
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Residues in contact with THR 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A VAL* 3.6 24.9 - - + -
248A MET 3.2 15.5 - - - +
249A THR* 2.7 26.0 + - - +
257A ALA* 3.9 5.4 + - - +
258A ALA* 1.3 73.1 + - - +
260A LYS* 1.3 65.4 + - - +
261A ILE* 4.9 1.3 - - + -
274A GLU* 3.8 2.6 - - - +
275A LEU* 2.9 54.1 + - + +
282A ILE* 3.5 21.7 + - + +
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Residues in contact with LYS 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A TRP* 3.4 66.1 - - + +
246A VAL 3.7 0.3 - - - +
247A VAL* 3.6 3.6 - - - +
248A MET* 2.8 35.9 + - - +
258A ALA* 3.9 4.8 + - - +
259A THR* 1.3 78.8 - - - +
261A ILE* 1.3 66.1 + - - +
262A ILE* 4.0 4.6 + - + -
272A ILE* 3.7 28.5 - - + -
273A GLU 3.2 11.7 - - - +
274A GLU* 3.9 25.6 + - - +
275A LEU 4.4 0.4 - - - +
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Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PRO* 4.3 6.3 - - + -
246A VAL 3.5 7.9 - - - +
247A VAL* 3.8 30.5 - - + -
259A THR* 4.9 3.6 - - + -
260A LYS* 1.3 79.2 - - - +
262A ILE* 1.3 62.9 + - - +
263A TYR* 3.5 38.1 - - + +
272A ILE* 3.5 3.1 - - - -
273A GLU* 2.8 36.3 + - - +
275A LEU* 5.2 3.8 - - + -
310A ILE* 4.5 18.2 - - + -
312A ILE* 4.3 14.6 - - + -
319A HIS* 3.7 33.2 - - + +
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Residues in contact with ILE 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ILE* 3.9 15.0 - - + -
225A TRP* 4.1 17.7 - - + -
245A PRO* 3.4 1.4 - - - +
246A VAL 2.8 35.5 + - - +
248A MET* 3.6 30.1 - - + -
260A LYS* 4.4 5.6 - - + -
261A ILE* 1.3 79.1 - - - +
263A TYR* 1.3 65.5 + - - +
264A PHE* 3.4 34.6 - - + -
269A ILE* 4.1 17.7 - - + -
271A LYS 3.5 9.4 - - - +
272A ILE* 4.1 23.6 - - + -
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Residues in contact with TYR 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A VAL* 4.0 7.4 - - + -
244A CYS 3.9 2.5 - - - -
245A PRO* 3.8 20.2 - - + -
261A ILE* 3.5 28.8 - - + +
262A ILE* 1.3 75.0 - - - +
264A PHE* 1.3 60.3 + - - +
269A ILE* 3.7 3.8 - - - -
270A GLN* 2.8 28.5 + - - +
271A LYS* 2.9 30.3 + - + +
273A GLU* 2.7 33.5 + - + -
312A ILE* 3.7 22.5 - - + +
313A ASP 4.5 0.7 - - - -
314A PRO* 4.9 0.4 - - + -
317A MET* 3.5 55.0 - - + -
318A THR 3.3 17.0 + - - -
319A HIS* 4.1 1.4 + - - +
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Residues in contact with PHE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A MET* 3.6 22.7 - - + -
199A ILE* 3.9 4.5 - - + -
212A VAL* 3.7 29.8 - - + -
222A ILE* 4.0 4.3 - - + -
242A GLY 3.4 0.7 - - - +
243A VAL* 3.2 5.9 - - - -
244A CYS* 2.7 50.8 + - + +
246A VAL* 3.8 22.7 - - + -
248A MET* 4.0 15.0 - - + -
262A ILE* 3.4 34.1 - - + -
263A TYR* 1.3 73.6 - - - +
265A LYS* 1.3 60.7 + - - +
267A GLY* 3.9 21.5 - - - +
268A LYS 3.4 11.2 - - - -
269A ILE* 3.8 20.6 - - + -
270A GLN* 4.2 2.0 - - - -
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Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PHE* 4.4 24.2 - - + -
241A LYS 4.7 5.2 + - - -
242A GLY* 3.3 25.6 - - - +
243A VAL* 4.7 9.0 - - + -
244A CYS* 5.9 0.4 - - - -
264A PHE* 1.3 75.1 - - - +
266A GLU* 1.3 83.7 + - + +
268A LYS* 2.9 24.5 + - - +
270A GLN* 3.7 28.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il